Evidence-Based Medicine (EBM) developed from the work of clinical epidemiologists at McMaster University and Oxford University in the 1970s and 1980s and self-consciously presented itself as a "new paradigm" called "evidence-based medicine" in the early 1990s. The techniques of the randomized controlled trial, systematic review and meta-analysis have produced an extensive and powerful body of research. They have also generated a critical literature that raises general concerns about its methods. This paper is a systematic review of the critical literature. It finds the description of EBM as a Kuhnian paradigm helpful and worth taking further. Three kinds of criticism are evaluated in detail: criticisms of procedural aspects of EBM (especially from Cartwright, Worrall and Howick), data showing the greater than expected fallibility of EBM (Ioaanidis and others), and concerns that EBM is incomplete as a philosophy of science (Ashcroft and others). The paper recommends a more instrumental or pragmatic approach to EBM, in which any ranking of evidence is done by reference to the actual, rather than the theoretically expected, reliability of results. Emphasis on EBM has eclipsed other necessary research methods in medicine. With the recent emphasis on translational medicine, we are seeing a restoration of the recognition that clinical research requires an engagement with basic theory (e.g. physiological, genetic, biochemical) and a range of empirical techniques such as bedside observation, laboratory and animal studies. EBM works best when used in this context